{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T07:23:22Z","timestamp":1769239402893,"version":"3.49.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3131,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Reliable structural modelling of protein\u2013protein complexes has widespread application, from drug design to advancing our knowledge of protein interactions and function. This work addresses three important issues in protein\u2013protein docking: implementing backbone flexibility, incorporating prior indications from experiment and bioinformatics, and providing public access via a server. 3D-Garden (Global And Restrained Docking Exploration Nexus), our benchmarked and server-ready flexible docking system, allows sophisticated programming of surface patches by the user via a facet representation of the interactors\u2019 molecular surfaces (generated with the marching cubes algorithm). Flexibility is implemented as a weighted exhaustive conformer search for each clashing pair of molecular branches in a set of 5000 models filtered from around \u223c340 000 initially.<\/jats:p>\n               <jats:p>Results: In a non-global assessment, carried out strictly according to the protocols for number of models considered and model quality of the Critical Assessment of Protein Interactions (CAPRI) experiment, over the widely-used Benchmark 2.0 of 84 complexes, 3D-Garden identifies a set of ten models containing an acceptable or better model in 29\/45 test cases, including one with large conformational change. In 19\/45 cases an acceptable or better model is ranked first or second out of 340 000 candidates.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.sbg.bio.ic.ac.uk\/3dgarden (server)<\/jats:p>\n               <jats:p>Contact: \u00a0v.lesk@ic.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn093","type":"journal-article","created":{"date-parts":[[2008,3,8]],"date-time":"2008-03-08T01:24:07Z","timestamp":1204939447000},"page":"1137-1144","source":"Crossref","is-referenced-by-count":60,"title":["3D-Garden: a system for modelling protein\u2013protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm"],"prefix":"10.1093","volume":"24","author":[{"given":"Victor I.","family":"Lesk","sequence":"first","affiliation":[{"name":"Division of Molecular Biosciences, Imperial College London, South Kensington, London SW72AZ, UK"}]},{"given":"Michael J. 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